Abstract

We examined the effects of habitat discontinuities on gene flow among puma (Puma concolor) populations across the southwestern USA. Using 16 microsatellite loci, we genotyped 540 pumas sampled throughout the states of Utah, Colorado, Arizona, and New Mexico, where a high degree of habitat heterogeneity provides for a wide range of connective habitat configurations between subpopulations. We investigated genetic structuring using complementary individual- and population-based analyses, the latter employing a novel technique to geographically cluster individuals without introducing investigator bias. The analyses revealed genetic structuring at two distinct scales. First, strikingly strong differentiation between northern and southern regions within the study area suggests little migration between them. Second, within each region, gene flow appears to be strongly limited by distance, particularly in the presence of habitat barriers such as open desert and grasslands. Northern pumas showed both reduced genetic diversity and greater divergence from a hypothetical ancestral population based on Bayesian clustering analyses, possibly reflecting a post-Pleistocene range expansion. Bayesian clustering results were sensitive to sampling density, which may complicate inference of numbers of populations when using this method. The results presented here build on those of previous studies, and begin to complete a picture of how different habitat types facilitate or impede gene flow among puma populations.

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Publication History

Issue online: 3 May 2005

Version of record online: 3 May 2005

Received 25 October 2004; revision accepted 1 March 2005

Supporting Information

Fig S1. Assignment of samples to populations using STRUCTURE with K = 9. Sample colors indicate assignment to nine population clusters; individuals that did not assign to any population with > 50% probability are shown in grey.Fig. S2. NMDS ordination of all 540 puma genotypes. Symbols indicate samples from northern region, southern region, and a transitional zone (AZ north of I-40 and the Manzano Mountains in NM), where samples did not consistently assign to northern or southern clusters using STRUCTURE or ordinations.Table. S1. Pairwise FST (upper diagonal) and DLR values between 34 sample groups. Underlined FST values were significant before Bonferroni correction (P < 0.05), and bold values remained significant after correction.

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